Prior to the establishment of bioRxiv, biological scientists were divided on the issue of having a dedicated preprint repository.[3] Many had concerns of having their research scooped by competitors and losing their claim to discovery. However, several geneticists had submitted papers to the "quantitative biology" section of the arXiv repository (launched in 2003) and no longer had those concerns, as they could point to preprints to support their claims of discovery.[3][9]

As a result of bioRxiv's popularity, several biology journals have updated their policies on preprints,[6][10] clarifying they do not consider preprints to be a 'prior publication' for purpose of the Ingelfinger rule. Over 20,000 tweets were made about bioRxiv-hosted preprints in 2015.[6] In July 2017, the number of monthly submissions exceeded 1,000.[11] As of October 21, 2018, over 30,000 papers have been accepted in total.[12]

A service called Rxivist combines preprints from bioRxiv with data from Twitter to rank pre-prints.[13]

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Jocelyn Kaiser of Science said that in their first year, the repository had "attracted a modest but growing stream of papers", having hosted 824 preprints.[10] As of February 2016, the submission rate to bioRxiv had steadily increased from ≈60 to ≈200 per month.[6] In 2017, the number of monthly submissions rose from over 800 in March [14] to more than 1000 in July[11] with a total number of 10,722 papers submitted in 2017.[15] By March 2018, the monthly rate of submissions increased to just under 1,500.[16]

The bioRxiv to Journals (B2J) initiative allows authors to submit their manuscript directly to a journal's submission system through bioRxiv. As of December 2018, 142 journals participate in the initiative.[2]